General O'Neill's Retirement
by De-gnome
Summary: General O'Neill retires to Atlantis, after DADT has been revoked. After one simple misunderstanding, Jack finds himself being isolated by the entire of Atlantis's population. And no, I would never make it that the members of SGA are bigots
1. Prologue: Just a Small Missunderstanding

The news that General O'Neill had beamed onto Atlantis spread like wildfire

The news that General O'Neill had beamed onto Atlantis spread like wildfire. It wasn't just the fact that the expedition had not heard the general was visiting, it was the fact that he was dropped of by an alien who 'just happened to be in the neighbourhood'.

When the news got to the gym John immediately stopped his fight with Teyla and headed for the control room, where the general had supposedly appeared. Lorne was already there greeting him.

When asked he just told Senior personnel that he had decided to retire to the beautiful city of Atlantis. Even if the galaxy was infested with 'space vampires'.

Even if the people had wanted to question him further he told them he was tired and just wanted to put his stuff down somewhere –he had just traveled from Earth's galaxy to another one called Othala before finally reaching Pegasus.

Jack remembered when the change began. Like every other day, He was in the control room. Just watching as the men and women were organizing out the rescue of Major Lorne's team, who had apparently missed check in by three hours. Jack knew as every other person or being experienced with gate travel, that that usually meant capture, being pinned down by an enemy, or some other disaster that their teams usually found themselves in. One of the technicians asked him the reason for him coming to Atlantis. Jack made the mistake of telling him too much, and yet at the same time, not telling him enough.

"I retired here because Don't ask, Don't Tell was about to be revoked, and Atlantis is the best place to retire off world."

The Canadian, who had up till then been quite pleasant, suddenly became engrossed in what he was doing, no longer initiating conversation. Jack just shrugged it off as a Canada/America thing.

However he soon found out how wrong he was. Project "Ignore Jack O'Niell" was started. It spread slowly, with the last contributor being Major Lorne. During conversations, the people would either ignore him, or if they were asked a direct question, they would give a very short answer.

Jack began counting down the days leading to the Apollo's arrival, with the knowledge that thee would be at lest one person aboard who would accept him.


	2. Jack's unwelcome rescue of offword teams

Firstly; The Disclaimer - I Do not own the characters or the shows in this story (unfortunately).

Secondly; Thanks to the reviewers - As always the reveiwing really helps

Thirdly; The previous chapter of this story was a prologue/introduction to the rest of the story - showing what triggered Jack to be isolated by the Atlantean Community

**Two weeks later.**

When Sheppard's team did not report in by their designated time for the second time inas many weeks, Major Lorne's team was again sent to rescue them from whatever trouble they had got themselves into. When Lorne's team also failed to report in, the expedition leader asked Jack to come out of retirement (for the second time, or third, if the incident on Tolana was to be counted).

After much coercing and pleading, Jack agreed to lead the team, although he was uneasy about it, as he knew the team would have to be extra vigilant on this mission in order prevent being compromised themselves. Jack remained concerned about the ability of the team he was leading to follow his orders, when they were so used to ignoring him.

His concern was so great that he actually asked the men if they were willing to follow his orders whilst they were out in the field, stressing that as soon as they go Sheppard or Lorne back, and they were in a condition to lead, he would relinquish command, as he _was_ after all retired. The marine that seemed to speak for the rest of the team replied, "Yes sir. We want the Colonel, the major, and the others back almost just as much as anyone. We would do just about anything to have them returned." The "_even put up with your command_" was left unspoken, just hanging in the air.

As it turned out the 'natives' of that planet had moved to that planet to avoid the wraith. However the city and surrounding towns that they now resided in had technology too advanced for even their greatest scientists. So when they had seen McKay fixing and analysing the technology, they 'kidnapped' him and used his team as a bargaining tool to make him work for them. When Lorne and his team entered the city, they also put them in the holding cell with the other three members of Sheppard's team.

Jack explained to the 'natives' that they would have willingly helped them, and that there were many other brilliant scientist back on their planet that would teach the 'natives' with the technology. He also assured the native that they would 'lend' them the scientists to teach them, only if the members of the expedition were released, a negotiation feat that he felt was worthy of Daniel himself.

Even after bringing home three gate teams, the only response he received was a short and forced "Thanks" only from a select few members of the teams.

What amazed Jack was how the scientist's would use him. Alongside John Sheppard, it became well known that Jack possessed the strongest ATA gene amongst any of the personnel in Atlantis. This made him an ideal switch and tester for the scientists.

However that was how far as it went. "Would you turn this on" "Could you activate this" "Please use this". He would try again and again to make conversation. At first asking questions like "so how fast can the Jumpers go?" Typical questions of an Airforce pilot like himself.

When this did not yield any results, he became so desperate to make conversation, he would ask questions about science. Yes science. To scientists. Jack had never thought he would have fallen so far. He could count on his fingers the times he asked scientific questions to either Sam or Daniel, and those were people he had work alongside for about nine years. And yet here he was trying – _and failing_ – to get these people to talk about something that they would usually spend the entire day talking about if you gave them half a chance.


	3. Jack's unwelcome rescue of scientists

Yet another time, both Lorne and Sheppard's teams were offworld, presumably one being sent off to rescue the other, and an alarm started blaring. Being in the Gateroom (he knew his presence irritated the people there, so Jack went there for what he saw was fair payback.), he could see that the alarm had originated from an area that had recently been designated for the scientists to work in.

Hurrying down to the 'lab' Jack quickly assessed the situation. It seemed like a cave in, and though the jumbled communications, he could discern that a science team was stuck inside the room and corridor. Unfortunately the panicking scientists were babbling so badly that Jack couldn't make out anything else. Grabbing a radio from a nearby soldier he spoke into it, "Shut up."

Silence descended from both sides of the cave in. Taking a breath, Jack spoke again "Now we need to know – how many of you are fine, how many are hurt, and how many, - if any – are dead."

A shaky voice replied "Lieutenant Tyrdren is dead, Zelenka and Matthews are unconscious and the rest of us – uh that's seven of us – all have some injuries."

"Now tell me how this happened"

"We were simply investigating some energy readings, but when we plugged our instruments in near the dials it sent out some sort of energy pulse. Lieutenant Tyrdren was closest to the controls. Zelenka was next closest – "

"I don't need to know that now." Jack interrupted, "What I need to know is – does anyone in there have resembling a degree in engineering?"

"Yes. Zelenka. But as I said he is unconscious at the moment."

Jack thought for a moment. "Does anyone have a degree in something to do with medicine?"

When the reply came over the radio, it was a completely different voice. "I do sir."

"Good. I need you to assess Dr Zelenka and tell me if he can be woken, and if so, could he give a true assessment of the damage, or if he is too concussed or something."

Silence reined as Jack hoped the medically inclined scientist woke and assessed Zelenka.

"Am awake. Dr Reichs says I am able to make proper judgment," a Czech voice came through the radio, "Ceiling has come down, but if top part of rubble is removed roof should remain stable."

"Should?"

"Ano. Should."

Jack turned to the soldiers standing of to the side. "Well you heard the man. Lets remove some of this rubble." Soon there was a human chain formed removing debris from the area the Czech had indicated. By the sounds coming from the opposite side, it seemed as though the scientists had begun to do the same thing. Within minutes, a small hole was formed, and a scientists face came into view. Jack climbed carefully to the top of the rubble and told him. "Just hold tight for a moment. We need to make the hole large enough to fit stretchers though." The Scientist nodded in understanding and disappeared, and the removal of the rubble resumed.

Once the hole was large enough, a nurse and a doctor went through, carrying collapsed stretchers. After waiting fro another few moments, two scientists made their way through the remaining rubble, carrying a stretcher in between them. Two other scientists followed, also carrying a stretcher. The third stretcher carried out was obviously the fallen Lieutenant, his body and face covered in a cloth. An airwoman rushed up to the stretcher and pulled back the cloth, revealing the young Lieutenant Tyrdren. _ Too young_. Jack thought

Jack marveled at how the men and women just stood and let the woman grieve for a man that, in another galaxy, she would not have been able to show any emotion about, without being court-martialed. And yet here they were, watching, with nothing but sorrow, pity and empathy on their faces. After what seemed like an age, the woman backed of slightly, and allowed the stretcher to be lifted to the medical bay, but remained with them.

After the Lieutenant's bhody had been carried off, Jack and the remaining personnel began to disperse. Jack took note of the number of people that seemed to want to say something to him, but stopped themselves. However, he did note with some pleasure that the remaining three scientists all managed to force out a 'thanks'.

Jack smirked at their discomfort. "Anytime."


	4. Jack's partner's welcome arrival

Just over a month after Jack had arrived in Atlantis, news spread that the Apollo was only a few days away from Atlantis. The excitement amongst the staff of the expedition was tangible. Each and every person was curious to know whether DADT was really being revoked, or if it was just a rumor. The excitement was such, that Jack actually had two whole sentences spoken to him, which he considered somewhat of a breakthrough.

Upon the Apollo's arrival, Jack wandered over to the disembarkation area, the designated beaming area that was at the moment alive with excited chatter. However, as his presence was noticed, silence fell. Rolling his eyes he made his way to a wall on the opposite side of the room to wait for the passengers.

As the arrivals began being beamed down, Jack began scanning the crowd. Spotting the person he was looking for he pushed off the wall and ambled over to them. Two hands grabbed his face, and pulled thim into a kiss, before the lecturing began, "I come back from offworld trip be told that you had retired – to another _galaxy_! And that it would be _three weeks_ until I could see my partner of _seven years_. And then, as if that wasn't enough, I find out that DADT had been revoked which, by the way, makes me wonder why the _hell _would you retire _now_ of all times."

Jack just smirked at the surprised and confused stares he was now receiving, and replied "I'll tell you later. So how were the brass reacting?" The two of them began walking from the Gateroom.

"To your retirement? They were overjoyed. To DADT being revoked? Completely and utterly annoyed."

"Well we kind expected a backlash from that. Those bigots always react to anything new or something that isn't completely conservative." Jack paused and kissed his partner.

"Was that an apology?"

"No. That was just because I finnally could," he told Daniel, grinning.


	5. Jack's acceptance into Atlantis

Once Daniel had unpacked, Jack began to give him a proper tour of Atlantis, as last time Daniel had only been able to see the 'hologram room'.

It amazed Jack at the speed at which things could turn around. As the two of them wandered through the corridors of Atlantis, people smiled (mostly guilty and/or sheepish) at Jack, and to his surprise one marine even came up to them and initiated a conversation. Jack marveled at the obvious speed of Atlantis's gossip mill – it was even faster than the SGC's. What he was also pleasantly surprised at was the ease at which the personnel were able to accept him once there was no obvious threat to Atlantis, or its favourite son..

Finally, Jack and Daniel entered the gym in time to see Sheppard's feet being swept out from under him by Teyla.

"Kind reminds me of you," Daniel told Jack.

"Don't be silly. I would never be so silly as to fight Teyla with those Stick things." Jack said, gesturing toward the bantos sticks, "I actually do have something resembling self preservation."

Daniel raised his eyebrows and was about to retort, but was beaten to it by Teyla, "I have heard through the Atlantis personnel that your disposition is much like John's. That our co-workers even believe that John is trying to keep up with your ability to annoy and make enemies of many races you meet."

"It's not my fault" Jack and John, protested in unison.

"Yeah just like the flings with random alien priestesses and other aliens?" Daniel asked Jack dryly. At this, Teyla gave John a look that could only be read as 'sound familiar?'

At the same time Jack frowned at Daniel and replied "And who exactly was it who had a _snake _after him?" At this both Teyla and John looked at Jack quizzically.

"Snake?"

"A go'auld" Jack explained. "Danny here had a goa'uld after him."

"Yeah I think that takes the cake," John agreed.

Teyla put a hand on John's arm and been her forehead forward to in the Athosian greeting. John lowered his, to greet her. She turned to Jack and Daniel and suggested "Perhaps I could continue to show Daniel around Atlantis?"

John looked at her gratefully.

Jack raised an eyebrow, but nodded, "Sure. That sounds great," he told her. Turning to Daniel he said "Danny – "

"I know, I know. Don't go running off, and don't go touching anything."

"And yet you are still going to do it" Jack mumbled even after Daniel was out of earshot.

Jack turned to Sheppard. "So…"

"So…"

Silence reigned for a few minutes, until it was broken by Jack. "You want to talk, I take it."

John smiled awkwardly. "Yeah. Well the thing is for the past few weeks or so- "

"Your people have been ignoring me on the basis that they thought I was a bigot and against same-sex relationships?"

John looked at feet embarrassed "Yeah. Well I kinda wanted to tell you that it wasn't- I mean I – "

"I know," Jack interrupted, saving John. He scrutinized the younger man. "I tell you what though, it is _amazing_ how loyal your people are"

John looked up, pleased to be hearing what he saw as due praise for Atlantis's personnel. "Yeah. They're really fantastic. The scientists save our butts on regular occasions, we try to protect them and so there is a great camaraderie spread throughout the expedition. I mean, some of the closest relationships are between a scientist and a marine."

"Or in you case, an airforce pilot."

John grinned, "Sir, if you knew Rodney and I were together, do you think others…" Sheppard drifted off.

"The thing is, Sheppard, I've spent the better part of seven years pretending to all but my closest friends that that I was not in love with an amazing person – that I was straight." Jack explained. "You cannot imagine my surprise when I saw a mirror image of us in two of the senior staff in Atlantis."

John grinned slightly, his gaze returning to his feet.

"You know it was Colonel Carter that got us together, right?"

"Carter, huh?" Jack smirked, "Yeah that sounds like her. How did she manage that?"

"She said that…" John looked up as realization dawned, "that she'd seen it before."

Jack laughed. "Yes that is definitely Carter. We even went so far as to pretend that Sam and I were – uh – cared for eachother, you know, more than we were supposed to. Now if you will excuse me, I will go find a certain wayward scientist, and I presume you will want to do the same," he continued as he and John headed down the corridor together.

"Yes sir. They're probably down at the science labs about now, tinkering with something dangerous."


	6. Jack's Second Apology

Jack watched as Daniel – the man he could now _openly_ call his boyfriend – walked away, talking to the scientist, or to himself, Jack couldn't tell.

Smiling softly to himself, he didn't hear Major Lorne come up behind him.

"Um, General?"

Jack turned "I keep telling you people. I'm retired. It's just Jack. Jack O'Neill. With two L's"

Lorne grinned, "So Jack..."

Jack raised an eyebrow. "Yes?"

"It seems that all of us in Atlantis got the wrong impression about you..."

"Really? I hadn't noticed."

"Yeah. Well you see sir" Jack raised his eyebrows at the title, "You said you retired because DADT had been revoked – "

"So you presumed I was a complete imbecile throwing a temper tantrum?"

Lorne gave a small grin. "Well yes, at the SGC, we could never find any signs…"

"Why were you looking for signs? Never mind, I don't want to know." Jack looked at the major for a while before continuing, "Anyway you were in the SGC before you came here, you should know I hate most of the regulations those idiots at the pentagon come up with."

"Yeah I suppose. But why _did_ you retire? And for that matter why did you retire _here_?"

Jack was silent before replying, "Both the president and I figured that there would be more chance of acceptance of DADT being revoked if I wasn't there."

"So it wouldn't seem like it was just for personal gain?"

"Ah. So not just a pretty face."

Lorne laughed. "Sorry sir. I'm straight. But seriously, why would you retire here? In a galaxy swarming with 'space vampires'?"

Jack shrugged, "because I am useless behind a desk, just pushing paperwork around. I need this excitement. And this" Jack gestured around them, "Well as Mitchell put it, this is Daniel Disneyland"

"You sound like John."

"So I've been told"

The End


End file.
